Handle checkpoints in a similar manner to how Trials of Osiris handles progress.
Pick up a Prison 'permit' and it gets a stamp according to which checkpoint you reach.
Players who haven't reached that checkpoint can't take part until they are within one checkpoint of the host. So players who are at the Pilot Servitor can run Skolas but not players who are lazy and want a freebie.
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Ooooooioo..... I likey....